{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "8ca19410",
   "metadata": {},
   "source": [
    "## Matched Molecular Series  \n",
    "### Introduction\n",
    "\n",
    "This notebook implements matched molecular series as described in these papers. \n",
    "\n",
    "Wawer, Mathias, and Jürgen Bajorath. \"Local structural changes, global data views: graphical substructure− activity relationship trailing.\" Journal of Medicinal Chemistry **54** (2011): 2944-2951. https://doi.org/10.1021/jm200026b\n",
    "\n",
    "O’Boyle, Noel M., Jonas Boström, Roger A. Sayle, and Adrian Gill. \"Using matched molecular series as a predictive tool to optimize biological activity.\" *Journal of Medicinal Chemistry*, **57** (2014): 2704-2713. [https://doi.org/10.1021/jm500022q](https://doi.org/10.1021/jm500022q)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "d49b756a",
   "metadata": {},
   "source": [
    "### Setup\n",
    "Check to see if we're running in Google Colab"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "c5ab3d33",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-05-05T22:15:42.001333Z",
     "start_time": "2025-05-05T22:15:41.998994Z"
    }
   },
   "outputs": [],
   "source": [
    "import sys\n",
    "IN_COLAB = 'google.colab' in sys.modules"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "63b2c026",
   "metadata": {},
   "source": [
    "Install the necessary Python packages"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "bc024f45",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-05-05T22:15:43.859663Z",
     "start_time": "2025-05-05T22:15:43.856185Z"
    }
   },
   "outputs": [],
   "source": [
    "%%capture\n",
    "if IN_COLAB:\n",
    "    !pip install pandas requests rdkit useful_rdkit_utils mols2grid"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c3c5e1b1",
   "metadata": {},
   "source": [
    "Download the scaffold_finder library from GitHub."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "d8ed6460",
   "metadata": {},
   "outputs": [],
   "source": [
    "if IN_COLAB:\n",
    "    import requests\n",
    "    lib_file = requests.get(\"https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/main/sar_analysis/scaffold_finder.py\")\n",
    "    ofs = open(\"scaffold_finder.py\",\"w\")\n",
    "    print(lib_file.text,file=ofs)\n",
    "    ofs.close()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "6d36ba33",
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "from rdkit import Chem\n",
    "from rdkit.Chem.rdMMPA import FragmentMol\n",
    "from rdkit.Chem.rdDepictor import Compute2DCoords\n",
    "from scaffold_finder import cleanup_fragment\n",
    "from operator import itemgetter\n",
    "import mols2grid\n",
    "from rdkit.Chem.TemplateAlign import AlignMolToTemplate2D"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "33f6005b",
   "metadata": {},
   "source": [
    "Useful utility functions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "f0a449c3",
   "metadata": {},
   "outputs": [],
   "source": [
    "def sort_fragments(mol):\n",
    "    \"\"\"\n",
    "    Transform a molecule with multiple fragments into a list of molecules that is sorted by number of atoms\n",
    "    from largest to smallest\n",
    "    \"\"\"\n",
    "    frag_list = list(Chem.GetMolFrags(mol, asMols=True))\n",
    "    frag_num_atoms_list = [(x.GetNumAtoms(), x) for x in frag_list]\n",
    "    frag_num_atoms_list.sort(key=itemgetter(0), reverse=True)\n",
    "    return [x[1] for x in frag_num_atoms_list]"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "045ec3c5",
   "metadata": {},
   "source": [
    "### Read Input\n",
    "Read the input data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "11e89097",
   "metadata": {},
   "outputs": [],
   "source": [
    "infile_url = \"../data/CHEMBL208.smi\"\n",
    "chembl208_df = pd.read_csv(infile_url,names=[\"SMILES\",\"Name\",\"pIC50\"])"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "83047b7a",
   "metadata": {},
   "source": [
    "Add an RDKit molecule to the dataframe"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "25138771",
   "metadata": {},
   "outputs": [],
   "source": [
    "chembl208_df['mol'] = chembl208_df.SMILES.apply(Chem.MolFromSmiles)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "67c211e9",
   "metadata": {},
   "source": [
    "### Generate Scaffold-Substituent Pairs\n",
    "Iterate over the molecules in the dataframe and transform to scaffold, substituent pairs "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "d453bde3",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>SMILES</th>\n",
       "      <th>Core</th>\n",
       "      <th>R_group</th>\n",
       "      <th>Name</th>\n",
       "      <th>pIC50</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>O=c1[nH]c2ccc(-c3cccc(Cl)c3)cc2s1</td>\n",
       "      <td>O=c1[nH]c2ccc([*:1])cc2s1</td>\n",
       "      <td>Clc1cccc([*:1])c1</td>\n",
       "      <td>CHEMBL94053</td>\n",
       "      <td>6.90</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>O=c1[nH]c2ccc(-c3cccc(Cl)c3)cc2s1</td>\n",
       "      <td>O=c1[nH]c2ccc(-c3cccc([*:1])c3)cc2s1</td>\n",
       "      <td>Cl[*:1]</td>\n",
       "      <td>CHEMBL94053</td>\n",
       "      <td>6.90</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>O=c1[nH]c2ccc(-c3cccc([N+](=O)[O-])c3)cc2n1Cc1...</td>\n",
       "      <td>O=c1[nH]c2ccc([*:1])cc2n1Cc1ccccc1</td>\n",
       "      <td>O=[N+]([O-])c1cccc([*:1])c1</td>\n",
       "      <td>CHEMBL327409</td>\n",
       "      <td>6.15</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>O=c1[nH]c2ccc(-c3cccc([N+](=O)[O-])c3)cc2n1Cc1...</td>\n",
       "      <td>O=c1[nH]c2ccc(-c3cccc([*:1])c3)cc2n1Cc1ccccc1</td>\n",
       "      <td>O=[N+]([O-])[*:1]</td>\n",
       "      <td>CHEMBL327409</td>\n",
       "      <td>6.15</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>O=c1[nH]c2ccc(-c3cccc([N+](=O)[O-])c3)cc2n1Cc1...</td>\n",
       "      <td>O=c1[nH]c2ccc(-c3cccc([N+](=O)[O-])c3)cc2n1[*:1]</td>\n",
       "      <td>c1ccc(C[*:1])cc1</td>\n",
       "      <td>CHEMBL327409</td>\n",
       "      <td>6.15</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3083</th>\n",
       "      <td>Cc1c(N[C@@H]2CCC[C@@]2(C)O)ccc(C#N)c1Cl</td>\n",
       "      <td>Cc1c(N[*:1])ccc(C#N)c1Cl</td>\n",
       "      <td>C[C@@]1(O)CCC[C@H]1[*:1]</td>\n",
       "      <td>CHEMBL3764185</td>\n",
       "      <td>6.06</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3084</th>\n",
       "      <td>Cc1c(N[C@@H]2CCC[C@@]2(C)O)ccc(C#N)c1Cl</td>\n",
       "      <td>Cc1c(N[C@@H]2CCC[C@]2(O)[*:1])ccc(C#N)c1Cl</td>\n",
       "      <td>C[*:1]</td>\n",
       "      <td>CHEMBL3764185</td>\n",
       "      <td>6.06</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3085</th>\n",
       "      <td>Cc1c(N[C@@H]2CCC[C@@]2(C)O)ccc(C#N)c1Cl</td>\n",
       "      <td>Cc1c(N[C@@H]2CCC[C@]2(C)[*:1])ccc(C#N)c1Cl</td>\n",
       "      <td>O[*:1]</td>\n",
       "      <td>CHEMBL3764185</td>\n",
       "      <td>6.06</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3086</th>\n",
       "      <td>Cc1c(N[C@@H]2CCC[C@@]2(C)O)ccc(C#N)c1Cl</td>\n",
       "      <td>Cc1c(N[C@@H]2CCC[C@@]2(C)O)ccc([*:1])c1Cl</td>\n",
       "      <td>N#C[*:1]</td>\n",
       "      <td>CHEMBL3764185</td>\n",
       "      <td>6.06</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3087</th>\n",
       "      <td>Cc1c(N[C@@H]2CCC[C@@]2(C)O)ccc(C#N)c1Cl</td>\n",
       "      <td>Cc1c(N[C@@H]2CCC[C@@]2(C)O)ccc(C#N)c1[*:1]</td>\n",
       "      <td>Cl[*:1]</td>\n",
       "      <td>CHEMBL3764185</td>\n",
       "      <td>6.06</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>3088 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                 SMILES  \\\n",
       "0                     O=c1[nH]c2ccc(-c3cccc(Cl)c3)cc2s1   \n",
       "1                     O=c1[nH]c2ccc(-c3cccc(Cl)c3)cc2s1   \n",
       "2     O=c1[nH]c2ccc(-c3cccc([N+](=O)[O-])c3)cc2n1Cc1...   \n",
       "3     O=c1[nH]c2ccc(-c3cccc([N+](=O)[O-])c3)cc2n1Cc1...   \n",
       "4     O=c1[nH]c2ccc(-c3cccc([N+](=O)[O-])c3)cc2n1Cc1...   \n",
       "...                                                 ...   \n",
       "3083            Cc1c(N[C@@H]2CCC[C@@]2(C)O)ccc(C#N)c1Cl   \n",
       "3084            Cc1c(N[C@@H]2CCC[C@@]2(C)O)ccc(C#N)c1Cl   \n",
       "3085            Cc1c(N[C@@H]2CCC[C@@]2(C)O)ccc(C#N)c1Cl   \n",
       "3086            Cc1c(N[C@@H]2CCC[C@@]2(C)O)ccc(C#N)c1Cl   \n",
       "3087            Cc1c(N[C@@H]2CCC[C@@]2(C)O)ccc(C#N)c1Cl   \n",
       "\n",
       "                                                  Core  \\\n",
       "0                            O=c1[nH]c2ccc([*:1])cc2s1   \n",
       "1                 O=c1[nH]c2ccc(-c3cccc([*:1])c3)cc2s1   \n",
       "2                   O=c1[nH]c2ccc([*:1])cc2n1Cc1ccccc1   \n",
       "3        O=c1[nH]c2ccc(-c3cccc([*:1])c3)cc2n1Cc1ccccc1   \n",
       "4     O=c1[nH]c2ccc(-c3cccc([N+](=O)[O-])c3)cc2n1[*:1]   \n",
       "...                                                ...   \n",
       "3083                          Cc1c(N[*:1])ccc(C#N)c1Cl   \n",
       "3084        Cc1c(N[C@@H]2CCC[C@]2(O)[*:1])ccc(C#N)c1Cl   \n",
       "3085        Cc1c(N[C@@H]2CCC[C@]2(C)[*:1])ccc(C#N)c1Cl   \n",
       "3086         Cc1c(N[C@@H]2CCC[C@@]2(C)O)ccc([*:1])c1Cl   \n",
       "3087        Cc1c(N[C@@H]2CCC[C@@]2(C)O)ccc(C#N)c1[*:1]   \n",
       "\n",
       "                          R_group           Name  pIC50  \n",
       "0               Clc1cccc([*:1])c1    CHEMBL94053   6.90  \n",
       "1                         Cl[*:1]    CHEMBL94053   6.90  \n",
       "2     O=[N+]([O-])c1cccc([*:1])c1   CHEMBL327409   6.15  \n",
       "3               O=[N+]([O-])[*:1]   CHEMBL327409   6.15  \n",
       "4                c1ccc(C[*:1])cc1   CHEMBL327409   6.15  \n",
       "...                           ...            ...    ...  \n",
       "3083     C[C@@]1(O)CCC[C@H]1[*:1]  CHEMBL3764185   6.06  \n",
       "3084                       C[*:1]  CHEMBL3764185   6.06  \n",
       "3085                       O[*:1]  CHEMBL3764185   6.06  \n",
       "3086                     N#C[*:1]  CHEMBL3764185   6.06  \n",
       "3087                      Cl[*:1]  CHEMBL3764185   6.06  \n",
       "\n",
       "[3088 rows x 5 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "row_list = []\n",
    "for smiles, name, pIC50, mol in chembl208_df.values:\n",
    "    frag_list = FragmentMol(mol,maxCuts=1)\n",
    "    for _,frag_mol in frag_list:\n",
    "        pair_list = sort_fragments(frag_mol)\n",
    "        row_list.append([smiles]+[Chem.MolToSmiles(x) for x in pair_list]+[name, pIC50])\n",
    "row_df = pd.DataFrame(row_list,columns=[\"SMILES\",\"Core\",\"R_group\",\"Name\",\"pIC50\"])\n",
    "row_df"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4b3a3b4c",
   "metadata": {},
   "source": [
    "### View Scaffolds\n",
    "Put the scaffolds into a dataframe"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "b09dc358",
   "metadata": {},
   "outputs": [],
   "source": [
    "scaffold_df = row_df.Core.value_counts().to_frame().reset_index()\n",
    "scaffold_df.columns = [\"SMILES\",\"Count\"]\n",
    "scaffold_df['mol'] = scaffold_df.SMILES.apply(Chem.MolFromSmiles)\n",
    "_ = scaffold_df.mol.apply(Compute2DCoords)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "84fc6ae1",
   "metadata": {},
   "source": [
    "Display the scaffolds"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "fc8c409d",
   "metadata": {},
   "outputs": [
    {
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       "MolGridWidget()"
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     "metadata": {},
     "output_type": "display_data"
    },
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       "#mols2grid, tr, td {\n",
       "    border: none;\n",
       "}\n",
       "#mols2grid tr {\n",
       "    page-break-inside: avoid !important;\n",
       "}\n",
       "\n",
       "/* Cell */\n",
       "#mols2grid td {\n",
       "    border: 1px solid #cccccc;\n",
       "    text-align: center;\n",
       "    vertical-align: top;\n",
       "    max-width: 130px;\n",
       "    width: 130px;\n",
       "    font-family: &#x27;DejaVu&#x27;, sans-serif;\n",
       "    font-size: 12px;\n",
       "    margin: 0;\n",
       "    padding: 10px;\n",
       "    position: relative;\n",
       "}\n",
       "\n",
       "/* Call focus state */\n",
       "#mols2grid td:focus-within,\n",
       "#mols2grid td:focus {\n",
       "    outline: solid 2px #555;\n",
       "    border-color: transparent;\n",
       "}\n",
       "\n",
       "/* ID */\n",
       "#mols2grid .data-mols2grid-id {\n",
       "    position: absolute;\n",
       "    top: 0;\n",
       "    left: 0;\n",
       "    padding: 5px;\n",
       "}\n",
       "\n",
       "/* Tooltip margin */\n",
       "/* Adjusted so it plays well with the extruded outline */\n",
       ".popover[x-placement] {\n",
       "    margin: 1px 2px 2px 1px;\n",
       "}\n",
       "\n",
       "\n",
       "#mols2grid td div img {\n",
       "    max-width: px;\n",
       "    width: px;\n",
       "    height: auto;\n",
       "    padding: 0;\n",
       "}\n",
       "\n",
       "            /* Custom CSS */\n",
       "            \n",
       "        &lt;/style&gt;\n",
       "        &lt;script src=&quot;https://code.jquery.com/jquery-3.5.1.slim.min.js&quot; integrity=&quot;sha384-DfXdz2htPH0lsSSs5nCTpuj/zy4C+OGpamoFVy38MVBnE+IbbVYUew+OrCXaRkfj&quot; crossorigin=&quot;anonymous&quot;&gt;&lt;/script&gt;\n",
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       "        // Only fit height when no specific height was given.\n",
       "        if (iframe.getAttribute(&#x27;height&#x27;)) return;\n",
       "\n",
       "        // Initial fit + refit whenever the window width changes.\n",
       "        _fit()\n",
       "        $(window).on(&#x27;resize&#x27;, function() {\n",
       "            if (window.innerWidth != window.prevInnerWidth) {\n",
       "                window.prevInnerWidth = window.innerWidth\n",
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       "            }\n",
       "        })\n",
       "\n",
       "        // Fit iframe height to content height.\n",
       "        function _fit() {\n",
       "            var height = iframe.contentDocument.body.scrollHeight + 18 + &#x27;px&#x27;;\n",
       "            iframe.style.height = height;\n",
       "        }\n",
       "    }\n",
       "&lt;/script&gt;\n",
       "\n",
       "&lt;!-- prettier-ignore --&gt;\n",
       "&lt;script src=&quot;https://cdn.jsdelivr.net/npm/bootstrap@4.6.0/dist/js/bootstrap.bundle.min.js&quot; integrity=&quot;sha384-Piv4xVNRyMGpqkS2by6br4gNJ7DXjqk09RmUpJ8jgGtD7zP9yug3goQfGII0yAns&quot; crossorigin=&quot;anonymous&quot;&gt;&lt;/script&gt;\n",
       "        \n",
       "        &lt;!-- Custom header --&gt;\n",
       "        \n",
       "\n",
       "\n",
       "\n",
       "\n",
       "    &lt;/head&gt;\n",
       "    &lt;body class=&quot;m2g-inside-iframe&quot;&gt;\n",
       "\n",
       "\n",
       "        &lt;table id=&quot;mols2grid&quot;&gt;\n",
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       "&lt;/svg&gt;\n",
       "&lt;/div&gt;\n",
       "&lt;div class=&quot;data copy-me data-mols2grid-id&quot;&gt;19&lt;/div&gt;\n",
       "&lt;div class=&quot;data copy-me data-Count&quot;&gt;9&lt;/div&gt;\n",
       "&lt;/div&gt;\n",
       "&lt;/td&gt;\n",
       "&lt;/tr&gt;\n",
       "            &lt;/tbody&gt;\n",
       "        &lt;/table&gt;\n",
       "\n",
       "        &lt;script&gt;\n",
       "            \n",
       "\n",
       "            // Set iframe height to fit content.\n",
       "            fitIframe(window.frameElement);\n",
       "        &lt;/script&gt;\n",
       "\n",
       "\n",
       "\n",
       "    &lt;/body&gt;\n",
       "&lt;/html&gt;\n",
       "\">\n",
       "</iframe>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mols2grid.display(scaffold_df.head(20),subset=[\"img\",\"Count\"],mol_col=\"mol\",\n",
    "                  use_coords=True,prerender=True,template=\"static\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "0377e44e",
   "metadata": {},
   "source": [
    "### View Matched Molecular Series  \n",
    "Set **idx** to the index from the scaffold table above to display molecules from that series  \n",
    "Set **clear_matches** to **False** to highlight the scaffold in the table below"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "43ea0640",
   "metadata": {},
   "outputs": [
    {
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       "version_minor": 0
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      "text/plain": [
       "MolGridWidget()"
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     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
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       "    \n",
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       "    &lt;head&gt;\n",
       "        &lt;meta charset=&quot;UTF-8&quot; /&gt;\n",
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       "    border-spacing: 0px;\n",
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      "text/plain": [
       "<IPython.core.display.HTML object>"
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     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "idx = 2\n",
    "clear_matches = False\n",
    "scaffold_smi = scaffold_df.SMILES.values[idx]\n",
    "scaffold_mol = scaffold_df.mol.values[idx]\n",
    "scaffold_mol = cleanup_fragment(scaffold_mol)[0]\n",
    "current_df = row_df.query(\"Core == @scaffold_smi\").sort_values(\"pIC50\",ascending=False).copy()\n",
    "current_df['mol'] = current_df.SMILES.apply(Chem.MolFromSmiles)\n",
    "for mol in current_df.mol.values:\n",
    "    AlignMolToTemplate2D(mol, scaffold_mol)\n",
    "    if clear_matches:\n",
    "        mol.__sssAtoms = []\n",
    "mols2grid.display(current_df,subset=[\"img\",\"pIC50\"],mol_col=\"mol\",use_coords=True,prerender=True,template=\"static\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "2fe2d318",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "87e790a3",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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